Ok, well I'm guessing I don't have root. Here's what I did:
Complete wipe of phone (fastboot or whatever back to stock). Installed the dual boot stuff, with a stock ICS rom in the default (safe) position. Rooted the rom, then created a slot for the JB rom. Installed JB, started the JB kernel and booted. Then I tried to gain root access and it didn't work. I'm still rooted on the ICS side, but can't get root on the JB rom. Did I miss something, can someone give me a detailed explanation of how to dual boot ICS and JB and keep the root in the JB side?
Thanks in advance, I can't find any instructions on how to do this anywhere..

I haven't tried to use JB in a rom slot. Here is what worked for me...

I flashed back to stock ICS and rooted. Then I used voodoo to save root. I used the stock recovery to flash stock JB. Here is where it gets a little weird. Voodoo couldn't restore root automatically, so I had to use the root restore tool that mattlgroff made for us (THANKS MATTLGROFF). You can find it and instructions for its use here [Leaked-Ota][Cdma][4.1.2] Jelly Bean 98.72.8 (12/27/12) - xda-developers

This restored my root. After I was up and running with rooted JB, I installed Safestrap and flashed this rom in rom slot 1.

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